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idekerlab / DCell

DCell browser and gene deletion simulator
http://d-cell.ucsd.edu/
MIT License
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yeast->human #35

Open animesh opened 6 years ago

animesh commented 6 years ago

what would be the recommended way to move the "dna repair" demo from yeast to human?

michaelkyu commented 6 years ago

This would be a non-trivial task because the current DCell model was trained on yeast. You would need to train a new DCell model using data in human cells.

animesh commented 6 years ago

ok, but what would it need in terms of input files? i have some free gpu time, can try to train, if could you tell me where to start from :)

majianzhu commented 6 years ago
  1. Prepare an ontology file to restrict the neural network structure. The file needs to have the same format as the example.
  2. Prepare a gene list to represent the gene deletions. Currently for memory issue, we only allow binary output. If you have any special real value input, please send me the file and I can help to adjust the code.
  3. Tune the hyper-parameters based on your data.
  4. Need some outside data to validate the state learned for each term as shown in the paper.